changeset 6:5ca4946f3950 draft

Deleted selected files

--- a/fasta_indexes.loc.sample	Wed Jun 04 09:54:36 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,29 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a fasta_indexes.loc file
-#similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The fasta_indexes.loc
-#file has this format (white space characters are TAB characters):
-#
-# <unique_build_id>	<dbkey>	<display_name>	<file_base_path>
-#
-#So, for example, if you had hg19 Canonical indexed stored in
-#
-# /depot/data2/galaxy/hg19/sam/,
-#
-#then the fasta_indexes.loc entry would look like this:
-#
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#
-#and your /depot/data2/galaxy/hg19/sam/ directory
-#would contain hg19canon.fa and hg19canon.fa.fai files.
-#
-#Your fasta_indexes.loc file should include an entry per line for
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#hg18canon	hg18	Human (Homo sapiens): hg18 Canonical	/depot/data2/galaxy/hg18/sam/hg18canon.fa
-#hg18full	hg18	Human (Homo sapiens): hg18 Full	/depot/data2/galaxy/hg18/sam/hg18full.fa
-#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/depot/data2/galaxy/hg19/sam/hg19canon.fa
-#hg19full	hg19	Human (Homo sapiens): hg19 Full	/depot/data2/galaxy/hg19/sam/hg19full.fa

--- a/softsearch.xml	Wed Jun 04 09:54:36 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,53 +0,0 @@
-<?xml version="1.0"?>
-<tool id="SoftSearch" name="SoftSearch">
-  <description>for structure variation</description>
-  <command>#if $source.index_source=="history" 
-	        samtools index $bam_file ; samtools faidx $source.history_fasta_file ; $inc | /home/plus91/2.4/src/SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.history_fasta_file -o $out_file1
-	    #else
-		samtools index $bam_file ; samtools faidx $source.ref_fasta.fields.path ; $inc | /home/plus91/2.4/src//2.4/src/SoftSearch.pl -l $min_length_soft_clip -q $min_map_quality -r $min_depth_soft_clip_loc -m $min_no_discordant_read -s $no_sd_consider_discordant -b $bam_file -f $source.ref_fasta.fields.path -o $out_file1
-	    #end if		
- </command>
-  <inputs>
-      <param name="bam_file" type="data"   format="bam" label="BAM Files" />
-	 <conditional name="source">
-            <param name="index_source" type="select" label="Choose the source for the reference list">
-                <option value="cached">Locally cached</option>
-                <option value="history">History</option>
-            </param>
-            <when value="history">
-                <param format="fasta" name="history_fasta_file" type="data" label="Fasta file from history."/>
-            </when>
-            <when value="cached">
-                  <param name="ref_fasta" type="select" >
-                    <options from_data_table="fasta_indexes">
-                    <validator type="no_options" message="No Fasta file is available" />
-                    </options>
-                  </param>
-            </when>
-        </conditional>
-      <param name="inc" type="hidden" value="n=$RANDOM" />
-     	<param name="min_length_soft_clip" type="integer" value="10" label="-l Minimum length of soft-clipped segment [5]" /> 
-        <param name="min_map_quality" type="integer" value="20" label="-q Minimum mapping quality [20]" /> 	
-	<param name="min_depth_soft_clip_loc" type="integer" value="10" label="-r Minimum depth of soft-clipped reads at position [5]" /> 
-	<param name="min_no_discordant_read" type="integer" value="10" label="-m Minimum number of discordant read pairs [5]" /> 
-	<param name="no_sd_consider_discordant" type="integer" value="4" label="-s Number of sd away from mean to be considered discordant" />       
-  </inputs>
-  <outputs>
-      <data format="vcf" name="out_file1" />
-  </outputs>
-  <help>
-  </help>
-</tool>
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